There is a wide range of congenital problems associated with Kabuki syndrome with large differences between affected individuals. Some of the common problems are heart defects (30%), urinary tract anomalies, hearing loss (50%), hypotonia, and postnatal growth deficiency (83%). Other characteristics include skeletal abnormality, joint laxity, short stature, and unusual dermatoglyphic patterns.[3] They often suffer from recurrent ear infections in infancy.

Also, children with Kabuki syndrome often have distinctive behavioural features. For example, 50% are described as unusually sociable, 30% as engaging in only minimal interaction with others, 74% as liking routine and 87% as having a happy disposition.

A few have normal intelligence, most of whom have learning difficulties such as struggling with fine motor, speech skills, and memory.